I bought a 2010 E550 coupe (fully maintained since new by MB of San Jose) with panoramic roof that had a lot of creaking and popping noises from the roof. After getting MB (Autohaus of Belmont, CA) to service and inspect it, they advised that it was a known problem (TSB has been issued) and would cost $1800 to fix as the car was 3 months out of warranty. They also wanted $200 to diagnose this 'known problem'.

I declined to have the work done and went home to look at it and found that the windshield was very loose. After reviewing the maintenance records, turns out that the windshield was replaced by MB (Smythe European of San Jose) a couple of years previously and they made a spectacularly poor job of it. The entire top part was not attached to the car at all, only the sides and bottom of the windshield were bonded. I could push the windshield forward so far I could get my fingers through the gap. I could have pushed the whole windshield one-handed completely out of the car with very little effort.

I called MB USA and expressed my concerns about safety of such a lousy installation and they just told me that as it was out of warranty and I was the second owner, they could do nothing.
I then called MB of San Jose and said the repair was substandard and dangerous, and they could not have been less interested. Basically, their standpoint was, 'it was repaired more than 12 months ago; if you want it doing again, it will be $1900 for the windshield and $1700 for the creaking roof.'

I then took the car to a local auto glass repair shop and they removed and reinstalled the same windshield with new glue for $125, which has completely eradicated all the roof squeaking and popping. Seems like the windshield is a structural rigidity component of the car, and when it is not properly bonded, the body flexes and causes squeaking of the panoramic roof.

Since then, I have carried out a major maintenance myself and found badly fitted maintenance parts for practically everything I inspected. E.g. wheel lug nuts torqued to over 200 ft-lb (needed to jump on a 36" breaker bar to remove them), incorrect transmission oil, brake fluid, coolant and engine oil levels, brake bleed valves massively over-tightened (caliper thread damaged), missing bolts from the skid pans under the engine, incorrect bolts in various places. The car looks like it was wrenched on by gorillas.

A quick takeaway from this is - Mercedes is out to gut you for every cent and will not back you up if there is an issue. The dealer maintenance is also no better than any back street shop and will cost a fortune. Learn to do it yourself or get a respected specialist to take care of maintenance.